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comparison mutation_analysis.xml @ 119:626a956f3811 draft

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Uploaded
author davidvanzessen
date Thu, 11 Aug 2016 10:35:52 -0400
parents e7b550d52eb7
children 31cca6d3722a
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118:ad7ca9c2b748 119:626a956f3811
18 <option value="unproductive">Unproductive: Keep "unproductive" and "unproductive (see comment)"</option> 18 <option value="unproductive">Unproductive: Keep "unproductive" and "unproductive (see comment)"</option>
19 <option value="remove_unknown">Remove "unknown" and "unknown (see comment)"</option> 19 <option value="remove_unknown">Remove "unknown" and "unknown (see comment)"</option>
20 <option value="dont_filter">Don't filter</option> 20 <option value="dont_filter">Don't filter</option>
21 </param> 21 </param>
22 <param name="filter_uniques" type="select" label="Filter unique sequences" help="See below for an example."> 22 <param name="filter_uniques" type="select" label="Filter unique sequences" help="See below for an example.">
23 <option value="yes">Remove uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3)</option> 23 <option value="remove">Remove uniques (Based on nucleotide sequence + C)</option>
24 <option value="yes_c">Remove uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3 + C)</option> 24 <option value="keep">Keep uniques (Based on nucleotide sequence + C)</option>
25 <option value="keep">Keep uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3)</option>
26 <option value="keep_c">Keep uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3 + C)</option>
27 <option value="no" selected="true">No</option> 25 <option value="no" selected="true">No</option>
28 </param> 26 </param>
29 <param name="unique" type="select" label="Remove duplicates based on" help="" > 27 <param name="unique" type="select" label="Remove duplicates based on" help="" >
30 <option value="AA.JUNCTION_V_subclass" selected="true">Top.V.Gene, CDR3.Seq, C region</option> 28 <option value="AA.JUNCTION_V_subclass" selected="true">Top.V.Gene, CDR3.Seq, C region</option>
31 <option value="AA.JUNCTION_subclass">CDR3.Seq, C region</option> 29 <option value="AA.JUNCTION_subclass">CDR3.Seq, C region</option>
38 <option value="60_55">>60% class and >55% subclass</option> 36 <option value="60_55">>60% class and >55% subclass</option>
39 <option value="70_0">>70% class</option> 37 <option value="70_0">>70% class</option>
40 <option value="60_0">>60% class</option> 38 <option value="60_0">>60% class</option>
41 </param> 39 </param>
42 <param name="empty_region_filter" type="select" label="Sequence starts at" help="" > 40 <param name="empty_region_filter" type="select" label="Sequence starts at" help="" >
43 <option value="FR1" selected="true">FR1 : exclude empty CDR1,FR2,CDR2,FR3</option> 41 <option value="FR1" selected="true">FR1: exclude empty CDR1,FR2,CDR2,FR3</option>
44 <option value="CDR1">CDR1: exclude empty FR2,CDR2,FR3</option> 42 <option value="CDR1">CDR1: exclude empty FR2,CDR2,FR3</option>
45 <option value="FR2">FR2: exclude empty,CDR2,FR3</option> 43 <option value="FR2">FR2: exclude empty CDR2,FR3</option>
46 </param> 44 </param>
47 <conditional name="naive_output_cond"> 45 <conditional name="naive_output_cond">
48 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?"> 46 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?">
49 <option value="yes">Yes</option> 47 <option value="yes">Yes</option>
50 <option value="no" selected="true">No</option> 48 <option value="no" selected="true">No</option>